MME p.Phe508=
c.1524C>T · VCV3624590
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00334%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.95 | GERP -1.2, phastCons 1 |
| Overall | ||
| CADD | 13.98 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00334%
Admixed American · 2/59,914 alleles
Filtering AF
0.000554%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000559%
9/1,610,138 alleles · very rare
exomes 8/1,458,090 · genomes 1/152,048 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00334% | 29,957 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,320 |
| African / African-American | 0.00134% | 74,766 |
| South Asian | 0.0011% | 90,940 |
| European (non-Finnish) | 0.00034% | 294,236 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- MME
- Protein
- p.Phe508=
- Coding
- c.1524C>T
- MANE Select
- NM_007289
- Type
- single nucleotide variant
- Location
- chr3:155148576 (GRCh38)
- Gene constraint
- LOEUF 0.931 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.25 · 16 PDB
- Residue 508
- the peptidase m13 domain; an α-helix
Similar variants
- MME c.1497+1G>A Likely pathogenic ★★ same type
- MME c.1497+1G>C Likely pathogenic ★★ same type
- MME c.160+2T>C Likely pathogenic ★★ same type
- MME c.1601+2T>C Likely pathogenic ★★ same type
- MME c.1781-2A>G Pathogenic/Likely pathogenic ★★ same type
- MME c.439+1G>A Likely pathogenic ★★ same type
- MME c.440-2A>C Pathogenic/Likely pathogenic ★★ same type
- MME c.536-1G>A Pathogenic/Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/mme-p-phe508 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown